This report documents unsupervised learning analyses of the model residuals for traits measured in white and black REGARDS subjects (documented in the ‘baseline.csv’ file downloaded from Suraju Sadeeq’s OneDrive). The following outcomes will be considered for inclusion as traits:

eGFR, documented as ‘EGFR_CKDEPI’, left ventricular hypertrophy: ‘lvh_main’, atrial fibrillation: ‘Afib_SR_ECG’, diabetes: ‘Diab_SRMed_glu’, lipidemia: ‘lipidemia_meds_labs’, myocardial infarction: ‘MI_SR_ECG’, CAD: ‘CAD_SR_ECG’, insulin, creatinine level: ‘Creatinine_urine’, albumin level: ‘Albumin_urine’, cystatin C level: ‘Cysc’, C-reactive protein: ‘Crp’, triglycerides: ‘Trigly’, glucose, LDL, HDL, DBP, SBP, cholesterol: ‘Cholest’, heart rate: ‘Heartrate’, stroke: ‘Stroke_SR’, depression (as scale): ‘CESD’.

Some variables are excluded based on inspection. CESD is highly skewed and does not appear to cohere to the Center for Epidemiological Studies - Depression scale, so it will be dropped. In this case, no subject has CESD>12, whereas the CES-D scale ranges from 0 to 60, and individuals are considered at risk for depression when the score exceeds 16.

Report the missing rate for each outcome Only one variable has missing rate >5%, which is insulin. Insulin will be dropped from consideration.

Outcome MissingProp
EGFR_CKDEPI 0.025
lvh_main 0.015
Diab_SRMed_glu 0.025
Lipidemia_meds_labs 0.027
Afib_SR_ECG 0.024
MI_SR_ECG 0.018
CAD_SR_ECG 0.019
insulin 0.268
Creatinine_urine 0.047
Albumin_urine 0.049
DBP 0.003
SBP 0.003
Cysc 0.043
Crp 0.042
Trigly 0.026
Glucose 0.025
Ldl 0.041
Hdl 0.032
Cholest 0.025
Heartrate 0.012
Stroke_SR 0.003

The following variables will be considered as covariates in the analysis: alcohol use ‘Alc_Use’, gender ‘Gender_x’, age ‘Age_x’, smoking ‘Smoke’, education ‘ED_Cat’, income ‘Income’, weight ‘Weight’, and race ‘Race_x’.

Report the missing rate for each covariate. Income is the only covariate missing at >5%; it will be dropped, and the other seven retained. A complete case analysis will be performed on all individuals non-missing for both the covariates and the outcomes.

Covariate MissingProp
Weight 0.000
Smoke 0.004
Alc_Use 0.000
ED_Cat 0.001
Income 0.123
Gender_x 0.000
Race_x 0.000
Age_x 0.000

The complete case analysis consists of 9290 subjects.

The following outcomes are binary (and thus, logistic regression will be used): LVH, Diabetes, Lipidemia, MI, CAD, Stroke. The frequency of the less common category for these binary outcomes is described below.

Outcome RareProp
lvh_main 0.134
Diab_SRMed_glu 0.269
Lipidemia_meds_labs 0.448
Afib_SR_ECG 0.078
MI_SR_ECG 0.109
CAD_SR_ECG 0.147
Stroke_SR 0.060

Calculate the coefficient of determination for each of the models to give a sense of how predictive each covariate is. For the logistic models, use AUROC. These plots are interpreted as follows: the point label represents the predictive accuracy of the model without that variable included.

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Assess clustering and PCs for full set of residuals.

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations
## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)
## Warning: did not converge in 10 iterations
## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)
## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations
## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)
## Warning: did not converge in 10 iterations
## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)

## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)
## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

Assess clustering and PCs for model residuals with each of the seven covariates held out.

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## [1] "Adjusted rand index, no Alcohol: 0.023"
## [1] "No Alcohol table of clustering results"
##    tempCovarValues
##     Current Never Past
##   1    2935  1887 1216
##   2     794   790  567
##   3     437   355  309
## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)
## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)
## Warning: did not converge in 10 iterations
## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)
## Warning: did not converge in 10 iterations

## [1] "Adjusted rand index, no Gender: 0.013"
## [1] "No Gender table of clustering results"
##    tempCovarValues
##        F    M
##   1  593  636
##   2 4738 3323
## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

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## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## [1] "Adjusted rand index, no Smoking: 0.007"
## [1] "No Smoking table of clustering results"
##    tempCovarValues
##     Current Never Past
##   1    1027  2825 2177
##   2     351   935  879
##   3     220   414  462
## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations
## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)
## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations
## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)
## Warning: did not converge in 10 iterations
## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)
## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## [1] "Adjusted rand index, no Education: 0.008"
## [1] "No Education table of clustering results"
##    tempCovarValues
##     College graduate and above High school graduate Less than high school
##   1                       1345                 1072                   564
##   2                        627                  614                   314
##   3                        445                  519                   417
##   4                        296                  280                   210
##    tempCovarValues
##     Some college
##   1         1182
##   2          618
##   3          513
##   4          274
## Warning: did not converge in 10 iterations
## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)
## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations
## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)
## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations
## Warning: Quick-TRANSfer stage steps exceeded maximum (= 464500)
## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## Warning: did not converge in 10 iterations

## [1] "Adjusted rand index, no Race: 0.042"
## [1] "No Race table of clustering results"
##    tempCovarValues
##        B    W
##   1 6781 1271
##   2  957  281